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- PDB-6rza: Cryo-EM structure of the human inner arm dynein DNAH7 microtubule... -

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Basic information

Entry
Database: PDB / ID: 6rza
TitleCryo-EM structure of the human inner arm dynein DNAH7 microtubule binding domain bound to microtubules
Components
  • Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain 7, axonemal,Cytoplasmic dynein 1 heavy chain 1
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsMOTOR PROTEIN / filament / complex
Function / homology
Function and homology information


axonemal dynein complex / inner dynein arm assembly / cilium-dependent cell motility / inner dynein arm / manchette / cilium movement / positive regulation of intracellular transport / positive regulation of spindle assembly / minus-end-directed vesicle transport along microtubule / establishment of spindle localization ...axonemal dynein complex / inner dynein arm assembly / cilium-dependent cell motility / inner dynein arm / manchette / cilium movement / positive regulation of intracellular transport / positive regulation of spindle assembly / minus-end-directed vesicle transport along microtubule / establishment of spindle localization / ATP-dependent microtubule motor activity, minus-end-directed / cytoplasmic mRNA processing body assembly / dynein light intermediate chain binding / regulation of metaphase plate congression / cytoplasmic dynein complex / dynein complex / retrograde axonal transport / dynein intermediate chain binding / nuclear migration / regulation of mitotic spindle organization / stress granule assembly / cytoplasmic microtubule organization / microtubule motor activity / microtubule-based movement / cytoplasmic microtubule / axon cytoplasm / cellular response to interleukin-4 / microtubule-based process / cilium / filopodium / structural constituent of cytoskeleton / neuron migration / microtubule cytoskeleton organization / positive regulation of cold-induced thermogenesis / nuclear envelope / cell cortex / double-stranded RNA binding / mitotic cell cycle / microtubule / GTPase activity / cell division / centrosome / axon / GTP binding / neuronal cell body / ubiquitin protein ligase binding / calcium ion binding / go:0005623: / ATP binding / cytosol / cytoplasm
Tubulin C-terminal domain / Dynein heavy chain, domain-1 / Tubulin, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / EF-Hand 1, calcium-binding site / Tubulin, conserved site / Beta tubulin, autoregulation binding site / Dynein heavy chain, domain-2 / Tubulin/FtsZ, C-terminal / Dynein heavy chain, coiled coil stalk ...Tubulin C-terminal domain / Dynein heavy chain, domain-1 / Tubulin, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / EF-Hand 1, calcium-binding site / Tubulin, conserved site / Beta tubulin, autoregulation binding site / Dynein heavy chain, domain-2 / Tubulin/FtsZ, C-terminal / Dynein heavy chain, coiled coil stalk / Dynein heavy chain region D6 P-loop domain / AAA+ ATPase domain / Tubulin/FtsZ, GTPase domain / Beta tubulin / Alpha tubulin / EF-hand domain / Dynein heavy chain, AAA module D4 / Dynein heavy chain / Tubulin / Dynein heavy chain AAA lid domain / Tubulin/FtsZ family, GTPase domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain, domain 2, C-terminal / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain 3, AAA+ lid domain / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain, C-terminal domain / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ, GTPase domain superfamily / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / P-loop containing nucleoside triphosphate hydrolase
Tubulin beta chain / Tubulin alpha-1B chain / Dynein heavy chain 7, axonemal / Cytoplasmic dynein 1 heavy chain 1
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsLacey, S.E. / He, S. / Scheres, S.H.W. / Carter, A.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_A025_1011 United Kingdom
Wellcome TrustWT210711 United Kingdom
CitationJournal: Elife / Year: 2019
Title: Cryo-EM of dynein microtubule-binding domains shows how an axonemal dynein distorts the microtubule.
Authors: Samuel E Lacey / Shaoda He / Sjors Hw Scheres / Andrew P Carter /
Abstract: Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain ...Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain (MTBD) at the end of a coiled-coil stalk. We address how cytoplasmic and axonemal dynein MTBDs bind microtubules at near atomic resolution. We decorated microtubules with MTBDs of cytoplasmic dynein-1 and axonemal dynein DNAH7 and determined their cryo-EM structures using helical Relion. The majority of the MTBD is rigid upon binding, with the transition to the high-affinity state controlled by the movement of a single helix at the MTBD interface. DNAH7 contains an 18-residue insertion, found in many axonemal dyneins, that contacts the adjacent protofilament. Unexpectedly, we observe that DNAH7, but not dynein-1, induces large distortions in the microtubule cross-sectional curvature. This raises the possibility that dynein coordination in axonemes is mediated via conformational changes in the microtubule.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
X: Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain 7, axonemal,Cytoplasmic dynein 1 heavy chain 1
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,83213
Polymers211,1435
Non-polymers3,6898
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17810 Å2
ΔGint-99 kcal/mol
Surface area62270 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 437
2010C1 - 437
1020B1 - 426
2020D1 - 426

NCS ensembles:
ID
1
2

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Components

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Protein , 3 types, 5 molecules XACBD

#1: Protein Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain 7, axonemal,Cytoplasmic dynein 1 heavy chain 1 / Cytoplasmic dynein heavy chain 1 / Dynein heavy chain / cytosolic / Axonemal beta dynein heavy ...Cytoplasmic dynein heavy chain 1 / Dynein heavy chain / cytosolic / Axonemal beta dynein heavy chain 7 / Ciliary dynein heavy chain 7 / Dynein heavy chain-like protein 2 / hDHC2 / Cytoplasmic dynein heavy chain 1 / Dynein heavy chain / cytosolic


Mass: 18133.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again ...Details: Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Dync1h1, Dhc1, Dnch1, Dnchc1, Dyhc, DNAH7, KIAA0944 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JHU4, UniProt: Q8WXX0
#2: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 48679.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / References: UniProt: Q2XVP4
#3: Protein Tubulin beta chain / Beta-tubulin


Mass: 47825.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / References: UniProt: P02554

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Non-polymers , 4 types, 8 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-TA1 / TAXOL / Paclitaxel


Mass: 853.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1DNAH7 microtubule binding domain bound to microtubulesCOMPLEX1, 2, 30MULTIPLE SOURCES
2DNAH7COMPLEX11RECOMBINANT
3tubulinCOMPLEX2, 31NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Sus scrofa (pig)9823
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 67.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0247 / Classification: refinement
EM software
IDNameVersionCategory
9REFMAC5model refinement
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41984 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
RefinementResolution: 5.4→195.3 Å / Cor.coef. Fo:Fc: 0.582 / SU B: 243.237 / SU ML: 2.563 / ESU R: 2.187
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.65846 --
Obs0.65846 99086 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 206.247 Å2
Baniso -1Baniso -2Baniso -3
1-10.15 Å2-5.81 Å22.79 Å2
2---7.84 Å2-1.25 Å2
3----2.31 Å2
Refinement stepCycle: 1 / Resolution: 5.402→195.3 Å / Total: 14908
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01215251
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.5171.64720731
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.0651860
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.94622.587804
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.447152514
ELECTRON MICROSCOPYr_dihedral_angle_4_deg17.3461591
ELECTRON MICROSCOPYr_chiral_restr0.1030.21997
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0211767
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it24.69918.9997461
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it41.66328.49314
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it30.53521.647790
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined76.62366245
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refinement-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A281000.08
12C281000.08
21B291400.07
22D291400.07
LS refinement shellResolution: 5.402→5.542 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.74 7461 -
Obs--100 %

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